relmbeta: Sample dataset from murine gut microbiome
In kylebittinger/qiimer: Work with QIIME Output Files in R

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The relmbeta dataset is taken from a mouse study where wild-type and RELMbeta knockout mice were fed either a normal or high-fat diet. The diet was observed to have a pronounced effect on the gut microbiome composition. The genotype also had an effect, but less so.

A data frame with 20 rows and 3 columns.

The bacterial 16S rDNA gene was sequenced using 454 FLX technology, producing about 26k reads. The reads were processed via the standard QIIME workflow, pick_de_novo_otus.py, which clustered the reads into 776 operational taxonomic units (OTUs). QIIME version 1.7.0 was used for the analysis.

The OTU table was filtered to remove OTUs appearing in only one sample. Following this, a single rarefaction was performed at a level of 500 reads per sample. The unweighted UniFrac distance was then computed for each pair of samples.

The relmbeta data frame lists the sample IDs, genotypes, and dietary assignments for the mice.

Hildebrandt et al. High-fat diet determines the composition of the murine gut microbiome independently of obesity. Gastroenterology 137, 1716 (2009).

kylebittinger/qiimer documentation built on May 20, 2019, 7:30 p.m.